Complex geometries such as folds and protrusions in various organs are formed by the wrinkling/buckling of flat epithelial sheets. This morphogenesis is considered to be triggered by mechanical instabilities between the epithelial sheet and the mesenchyme foundation, similar to that observed in non-living film-on-substrate structures. Here, we report a film-on-substrate cell culture system (FoSS), in which the cells can induce wrinkling and buckling-delamination of the surface layer from the foundation. Ion beam irradiation on polylactic acid (PLA) produced three layers: a crosslinked/carbonized surface, a decomposed middle layer that undergoes solation under the cell culture condition, and a foundation. This system was realized by controlling the three-dimensional (3D) distributions of scission/crosslinking probabilities in PLA. Madin-Darby canine kidney epithelial cells adhered well to the surface layer of FoSS. Cellular forces caused the layer to become wrinkled and subsequently delaminated as a thin film (~165 nm) from the foundation. The cell population then crumpled the peeled films, and within 48 h formed 3D cell sheets with folds and protrusions depending on patterns pre-set on the FoSS. FoSS can be utilized to produce in vitro models of 3D morphogenesis and 3D cell sheets that are currently in demand for tissue engineering and regenerative medicine.